Identifying transition points in chemical reactions

ABSTRACT

An apparatus for identifying transition points in a chemical reaction, the apparatus comprising: a property value receiver, configured to receive a plurality of values of a physical property of the chemical reaction, a linear function calculator, associated with the property value receiver, configured to calculate a linear function connecting two of the received values, the two values pertaining to a start and end of a time period, a difference calculator, associated with the linear function calculator, configured to calculate a difference between the linear function and a plurality of the received values pertaining to the time period, and a transition point identifier, associated with the difference calculator, configured to identify at least one transition point of the chemical reaction, using the calculated difference.

This application is a continuation of U.S. patent application Ser. No.13/394,440, filed Mar. 6, 2012, now U.S. Pat. No. 11,072,821, which isthe U.S. national phase of International Patent Application No.PCT/IB2009/053997, filed Sep. 12, 2009.

FIELD AND BACKGROUND OF THE INVENTION

The present invention relates to analyzing, monitoring and controllingchemical reactions and, more particularly, but not exclusively tosystems and method for identifying transition points in chemicalreactions such as PCR (Polymerase Chain Reaction).

Chemical reaction may need to be characterized in real-time.

For example, detection and quantification of a molecule in a chemicalreaction may be required to take place as the reaction progresses, inorder to characterise the pattern of the reaction, take certain stepswhen the reaction moves into a new phase, etc.

Of special interest are a point of exponential growth of the chemicalreaction product and a point where growth of the product begins to slowto a halt, also referred to as elbow points. The elbow points may beused to determine whether any reaction products have been produced. Themagnitude of the reaction may be determined using a measured physicalproperty of the reaction, say photometric measurements between the elbowpoints, as described in further detail hereinbelow.

One widely used and well-established laboratory technique is PolymeraseChain Reaction (PCR).

In PCR, the polymerase enzyme attaches to a target DNA sequence andreplicates it exactly along with its containing chromosome or DNAstrand. If the target DNA sequence is not present or for some reason isunavailable for attachment to the PCR enzyme, no replication of DNAtakes place. This procedure is repeated many times in a PCR reactioninstrument. Thus, the target DNA sequence, as well as overall DNAconcentration, is amplified to microgram levels to allow for accuratedetection and data analysis.

Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR) is a widelyused PCR method. QF-PCR is commonly used for diagnosis and research infields such as disease (infectious or inherited), blood screenings,histology, oncology, tissue typing and drug discovery.

In QF-PCR, phosphate groups are introduced into the PCR reaction inorder to mark the replicated molecules for purposes of real-timedetection and quantification.

The two common methods for QF-PCR are: 1) Fluorescent dyes thatintercalate with double-stranded DNA and 2) Modified DNA probes thatfluoresce only when hybridised with the target DNA sequence, as known inthe art.

The latter method is more sensitive and therefore more reliable andaccurate, it also allows for real-time quantification of multiple DNAsequences using differently coloured probes.

The data received is in the form of fluorescent intensity, called FI.

The FI data may be represented using a graph. The shape of the graph maybe either linear (if a target DNA sequence was not found or notamplified) or appear to be a sigmoid curve (if the target sequence DNAwas amplified).

In case of presence of the target DNA sequence, there arises a need toidentify the point where amplification of the DNA sequence begins totake place, also referred to as the threshold point or C_(T). However,the FI data in the threshold's region usually has a low Signal to NoiseRatio (SNR). Consequently, determining C_(T) with a high degree ofaccuracy requires a method or a combination of methods for refining theFI data.

In photometric methods such as QF-PCR, photometry is utilised forreal-time detection and quantification of a reaction product.

In order to determine whether a) any reaction products have beenproduced, and b) the magnitude of production, targeted photoactiveprobes are utilised in the chemical reaction, to produce a photometriceffect (i.e. light) detectable by an optical sensor. The magnitude ofthe production is derived from data pertaining to the intensity of thephotometric effect.

Determining whether any reaction products have been produced, and themagnitude the production accurately is limited by the amount of noise inthe recorded photometric data. The noise may originate from chemicalsources, such as the reaction mix, as well as from electronic sources,such as the instrument used for light detection.

Several traditional methods have been used to determine time points ofexponential growth on a graph representing a quantitative measurement ofa chemical reaction over time.

One traditional method involves an n-derivative of light intensity usedto determine time periods of exponential growth.

International Patent Application No.: PCT/US2002/031144, to Taylor etal., published on Apr. 10, 2003, entitled “Adaptive baseline algorithmfor quantitative”, describes baseline subtraction algorithms developedto reduce tube-to-tube and cycle-to-cycle variabilities during real timePCR amplification. Particularly, Taylor describes an algorithm fordetermining a threshold cycle, for detection of an amplified nucleicacid production.

U.S. patent application Ser. No. 11/645,964, to Woo et al., filed onDec. 27, 2006, entitled “Automatic threshold setting and baselinedetermination for real-time PCR”, discloses a method which involves abase-lining operation, for identifying the bounds of a baseline regionand performing a linear interpolation to identify the characteristicequation defining the baseline.

US Patent Publication No. 20070148632, to Kurnik et al., describesSystems and methods for determining characteristic transition valuessuch as elbow values in sigmoid or growth-type curves, utilizing aLevenberg-Marquardt (LM) regression process.

U.S. patent application Ser. No. 11/861,188, to Kurnik et al., filed onSep. 25, 2007, entitled “PCR elbow determination using curvatureanalysis of a double sigmoid”, describes a method utilizing a first orsecond degree polynomial curve that fits the a growth type curve, anddetermination of a statistical significance value for the curve fit. Thesignificance value indicates whether the data represents significant orvalid growth.

Some traditional methods based on linear regression, are used todetermine the time point where growth in light intensity changes fromlinear to exponential. Typically, the linear regression based methodsinclude prior setting of a threshold for intensity, to determine thestart of exponential growth.

A particular method involving two-phase regression is described in anarticle by Edna Schechtman, published in the Journal of StatisticalComputation and Simulation, volume 17, issue 3, 1983 (pages 223-229),entitled “Inference in Two-Phase Regression: A Simulation study withNon-normal Observation”.

Some currently used methods involve converting data into a graph imageand rotating the image.

In a one example, U.S. patent application Ser. No. 11/349,538, toKurnik, filed on Feb. 6, 2006, entitled “PCR elbow determination byrotational transform after zero slope alignment”, describes PCR data setvisualization in a two-dimensional plot of fluorescence intensity vs.cycle number. Then, the PCR data set is adjusted to have a zero slope.

In a second example, Japanese Patent Publication No. 2007128483, toKurnik, published on May 24, 2007, entitled “PCR elbow determination byrotational transform”, describes a rotation transform application to amodified data set, to rotate the data about a defined coordinate such asthe origin, so that the data point representing the Ct value may becomea minimum or a maximum along the intensity axis. The data pointrepresenting the elbow or Ct value of the curve is identified, and thisdata point is then reversed back and the cycle number of the data pointis displayed.

U.S. patent application Ser. No. 11/423,377, to Kurnik, filed on 9,2006, entitled “CT determination by cluster analysis with variablecluster endpoint”, describes PCR data set visualized in atwo-dimensional plot of fluorescence intensity (y-axis) vs. cycle number(x-axis). Then, the points of the plot are clustered. Using theidentified clusters, a linear slope of each of the clusters isdetermined and the data point representing the elbow or Ct value of thePCR curve is identified as an end point of one of the identifiedclusters.

Other Methods, such as the one disclosed by Wittwer et al., in U.S. Pat.No. 6,503,720, combine two or more of the methods described hereinabove.

SUMMARY OF THE INVENTION

According to one aspect of the present invention there is provided anapparatus for identifying transition points in a chemical reaction, theapparatus comprising: a property value receiver, configured to receive aplurality of values of a physical property of the chemical reaction, alinear function calculator, associated with the property value receiver,configured to calculate a linear function connecting two of the receivedvalues, the two values pertaining to a start and end of a time period, adifference calculator, associated with the linear function calculator,configured to calculate a difference between the linear function and aplurality of the received values pertaining to the time period, and atransition point identifier, associated with the difference calculator,configured to identify at least one transition point of the chemicalreaction, using the calculated difference.

According to a second aspect of the present invention there is provideda computer implemented method for identifying transition points in achemical reaction, the method comprising steps the computer isprogrammed to perform, the steps comprising: a) receiving a plurality ofvalues of a physical property of the chemical reaction, b) calculating alinear function connecting two of the received values, the two valuespertaining to a start and end of a time period, c) calculating adifference between the linear function and a plurality of the receivedvalues pertaining to the time period, and d) identifying at least onetransition point of the chemical reaction, using the calculateddifference.

According to a third aspect of the present invention there is provided acomputer readable medium storing computer executable instructions forperforming steps of identifying transition points in a chemicalreaction, the steps comprising: a) receiving a plurality of values of aphysical property of the chemical reaction, b) calculating a linearfunction connecting two of the received values, the two valuespertaining to a start and end of a time period, c) calculating adifference between the linear function and a plurality of the receivedvalues pertaining to the time period, and d) identifying at least onetransition point of the chemical reaction, using the calculateddifference.

According to a fourth aspect of the present invention there is provideda system for identifying transition points in a chemical reaction, theapparatus comprising: a chemical reaction apparatus, comprising at leastone sensor configured to measure a plurality of values of a physicalproperty of a chemical reaction, a property value receiver, associatedwith the chemical reaction apparatus, configured to receive theplurality of values of the physical property of the chemical reaction, alinear function calculator, associated with the property value receiver,configured to calculate a linear function connecting two of the receivedvalues, the two values pertaining to a start and end of a time period, adifference calculator, associated with the linear function calculator,configured to calculate a difference between the linear function and aplurality of the received values pertaining to the time period, and atransition point identifier, associated with the difference calculator,configured to identify at least one transition point of the chemicalreaction, using the calculated difference.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. The materials, methods, andexamples provided herein are illustrative only and not intended to belimiting.

Implementation of the method and system of the present inventioninvolves performing or completing certain selected tasks or stepsmanually, automatically, or a combination thereof. Moreover, accordingto actual instrumentation and equipment of preferred embodiments of themethod and system of the present invention, several selected steps couldbe implemented by hardware or by software on any operating system of anyfirmware or a combination thereof. For example, as hardware, selectedsteps of the invention could be implemented as a chip or a circuit. Assoftware, selected steps of the invention could be implemented as aplurality of software instructions being executed by a computer usingany suitable operating system. In any case, selected steps of the methodand system of the invention could be described as being performed by adata processor, such as a computing platform for executing a pluralityof instructions.

BRIEF DESCRIPTION OF THE DRAWINGS

The invention is herein described, by way of example only, withreference to the accompanying drawings. With specific reference now tothe drawings in detail, it is stressed that the particulars shown are byway of example and for purposes of illustrative discussion of thepreferred embodiments of the present invention only, and are presentedin order to provide what is believed to be the most useful and readilyunderstood description of the principles and conceptual aspects of theinvention. The description taken with the drawings making apparent tothose skilled in the art how the several forms of the invention may beembodied in practice.

In the drawings:

FIG. 1 is a block diagram schematically illustrating an apparatus foridentifying transition points in a chemical reaction, according to anexemplary embodiment of the present invention.

FIG. 2 is a block diagram schematically illustrating a system foridentifying transition points in a chemical reaction, according to anexemplary embodiment of the present invention.

FIG. 3 is a flowchart schematically illustrating a method foridentifying transition points in a chemical reaction, according to anexemplary embodiment of the present invention.

FIGS. 4A, 4B, 4C, 4D and 4E are exemplary graphs, illustrating anexemplary scenario of identifying transition points in a chemicalreaction, according to an exemplary embodiment of the present invention.

FIG. 5 is a block diagram schematically illustrating a computer readablemedium storing computer executable instructions for performing steps ofidentifying transition points in a chemical reaction, according to anexemplary embodiment of the present invention.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

The present embodiments comprise a system and method for identifyingtransition points in a chemical reaction.

For example, a point of exponential growth of the chemical reaction'sproduct and a point where growth of the product begins to slow to a haltare referred to as elbow points. The elbow points may be used todetermine whether any reaction products have been produced, as well asto determine the magnitude of the chemical reaction, as described infurther detail hereinabove.

According to an exemplary embodiment of the present invention, one ormore transition points of a chemical reaction are identified, using alinear function.

The linear function connects two values of a physical property of thechemical reaction, say photometric values measured by sensors installedin proximity of a PCR reaction chamber, during a PCR process. The twovalues pertain to a start and an end of a time period of the chemicalreaction, respectively.

In order to identify the transition points, there is calculated adifference between the linear function and values of the physicalproperty between the two values connected by the linear function (i.e.values measured between the start and end of the time period).

The calculated difference serves to emphasize phase transitions of thechemical reaction, which are non-linear, and are usually substantiallyexponential.

The phase transitions are emphasized since the linear function's sloperepresents a nearly average rate of the chemical reaction during thetime period between the two points that the linear function connects.

That is to say that a comparison with the linear function helps identifythe transition points of the chemical reaction. The transition pointsare thus characterized by a reaction rate which substantially deviatesfrom the nearly average rate of the chemical reaction, as represented bythe slope of the calculated linear function.

Having identified the transition point(s) of the chemical reaction, asystem according to an exemplary embodiment, may provide a user (say alaboratory technician who operates a PCR Apparatus) with monitoring databased on the identified transition point(s).

The system according to an exemplary embodiment, may further initiate acontrol operation (say cooling of a chamber where the chemical reactiontakes place) upon identifying the transition point(s), etc., asdescribed in further detail hereinbelow.

The principles and operation of a system and method according to thepresent invention may be better understood with reference to thedrawings and accompanying description.

Before explaining at least one embodiment of the invention in detail, itis to be understood that the invention is not limited in its applicationto the details of construction and the arrangement of the components setforth in the following description or illustrated in the drawings. Theinvention is capable of other embodiments or of being practiced orcarried out in various ways. Also, it is to be understood that thephraseology and terminology employed herein is for the purpose ofdescription and should not be regarded as limiting.

Reference is now made to FIG. 1, which is a block diagram schematicallyillustrating an apparatus for identifying transition points in achemical reaction, according to an exemplary embodiment of the presentinvention.

Apparatus 1000 for identifying transition points in a chemical reactionmay be implemented using electric circuits, computer instructions, etc.The apparatus 1000 may be implemented on a dedicated computer, on acomputer chip connectable to a laboratory device (say to a PCRapparatus, as known in the art) or installable thereon, on acomputerized controller (say a computerized controller used in achemical factory), etc.

Optionally, the chemical reaction is a Polymerase Chain Reaction (PCR),say a Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR).

The apparatus 1000 includes a property value receiver 110.

The property value receiver 110 receives values of a physical propertyof the chemical reaction.

Optionally, the property value receiver 110 receives the physicalproperty values from thermometric sensors installed inside a chamberwhere the chemical reaction takes place, from photometric sensorsdeployed in proximity to the chamber, or from other devices, asdescribed in further detail hereinbelow.

For example, the chemical reaction may be a Quantitative FluorescentPolymerase Chain Reaction (QF-PCR). The Quantitative FluorescentPolymerase Chain Reaction is subjected to photometric measurements oflight emitted from the QF-PCR reaction chamber, during the chemicalreaction inside the QF-PCR chamber. The photometric measurement's valuesare then input to the property value receiver 110.

Optionally, the apparatus 1000 further includes one or more photometricmeasurement devices, say photo sensors installed in proximity to achamber where the chemical reaction takes place. The photometricmeasurement devices are in communication with the property valuereceiver 110, for providing the property value receiver 110 with thevalues, as measured by the photometric measurement devices while thechemical reaction progresses.

The apparatus 1000 further includes a linear function calculator 120.

The linear function calculator 120 is in communication with the propertyvalue receiver 110.

The linear function calculator 120 calculates a linear functionconnecting two of the received values. The two values pertain to a startand end of a time period, as described in further detail hereinbelow.

The time period may be a time period the chemical reaction is supposedto last for, a time period when a part of the chemical reaction takesplace, a time period long enough for the reaction to happen, a timeperiod spanning several cycles of the chemical reaction, etc.

Optionally, the linear function calculator 120 further allows a user ofthe apparatus 1000, to define the start and end of the time period, sayby inputting data defining the time period in absolute (say from 10:00PM to 10:15 PM) or relative (say 15 minutes from start) terms.

The apparatus 1000 further includes a difference calculator 130, incommunication with the linear function calculator 120.

The difference calculator 130 calculates a difference between the linearfunction and two (or more) of the received values that pertain to thetime period. For example, the difference calculator 130 may calculate adifferences between the linear function and a curve based on the receivevalues, over a time period of the chemical reaction (or a segmentthereof), as described in further detail hereinbelow.

Apparatus 1000 further includes a transition point identifier 140, incommunication with the difference calculator 130.

The transition point identifier 140 identifies one or more transitionpoints of the chemical reaction, using the calculated difference, asdescribed in further detail hereinbelow. For example, the transitionpoint identifier 140 may identify the transition points, by finding thepoints where the difference between the linear function and the receivedvalues is maximal, minimal, etc.

Optionally, at least one of the transition points identified by thetransition point identifier 140 is a point in time of the chemicalreaction, when the value of the physical property starts increasingsubstantially exponentially.

Optionally, at least one of the transition points identified by thetransition point identifier 140 is a point in time of the chemicalreaction, when the value of the physical property stops increasingsubstantially exponentially.

Optionally, at least one of the transition points identified by thetransition point identifier 140 is a point in time of the chemicalreaction, when the value of the physical property starts decreasingsubstantially exponentially.

Optionally, at least one of the transition points identified by thetransition point identifier 140 is a point in time of the chemicalreaction, when the value of the physical property stops decreasingsubstantially exponentially.

Optionally, the apparatus 1000 also includes a phase indicator, incommunication with the transition point identifier 140.

Optionally, when the transition point is identified, the phase indicatorindicates a beginning of a phase of the chemical reaction, an end of aphase of the chemical reaction, an end of a preliminary stabilizationphase of the chemical reaction, or any combination thereof.

Optionally, the apparatus 1000 further includes a control operationinitiator, in communication with the transition point identifier 140.

When the transition point is identified, the control operation initiatorinitiates a control operation. The control operation may include, but isnot limited to: initiating cooling of a chamber where the chemicalreaction takes place, opening of a pressure valve of a reaction chamber,instructing a PCR Robot to stop rotating, etc., as known in the art.

Optionally, the apparatus 1000 further includes a monitoring datagenerator, in communication with the transition point identifier 140, asdescribed in further detail hereinbelow.

The monitoring data generator generates monitoring data based on theidentified transition point(s).

Optionally, the monitoring data generator further presents the generateddata to a user, say using a computer screen, an SMS (Short MessagesService) message on a cellular phone used by the user, a message on aportable computer device such as a personal digital assistant (PDA), ora notebook computer, etc.

Reference is now made to FIG. 2, which is a block diagram schematicallyillustrating a system for identifying transition points in a chemicalreaction, according to an exemplary embodiment of the present invention.

A system according to an exemplary embodiment of the present inventionincludes a chemical reaction apparatus 2000.

Optionally, the chemical reaction apparatus 2000 includes a reactionchamber 210, where a chemical reaction (say PCR) takes place.

Optionally, the chemical reaction apparatus 2000 further includes one ormore sensors 230, for measuring values of a physical property of thechemical reaction.

For example, the sensors 230 may be photometric sensors installed inproximity of the reaction chamber 210. The photometric sensors measureintensity of light emitted from the reaction chamber 210, as thechemical reactions progresses.

The photometric sensors measure the emission of light from the reactionchamber, using standard fluorescence methods, as known in the art.

The chemical reaction apparatus 2000 may further include a cycle counter235, connected to the sensors 230. The cycle counter 235 instructs thesensors 230 to take measurement of the physical property, say once in aninterval of time. Optionally, the interval of time is predefined by auser, as known in the art.

The chemical reaction apparatus 2000 may further include anAnalog-to-Digital (A2D) converter 240, connected to the sensors 230. TheAnalog-to-Digital (A2D) converter 240 converts the measured values ofthe physical property of the chemical reaction to a digital format.

The System of FIG. 2 further includes a data accumulator 270, incommunication with the A2D converter 240.

The data accumulator 270 receives the measured values from the A2Dconverter 240, and stores the measured values.

The data accumulator 270 may include, but is not limited to a CD-ROM, aFlash Memory, a RAM (Random Access Memory), etc., as known in the art.

The system may further include apparatus 1000, as described in furtherdetail hereinabove.

Apparatus 1000 may be implemented using electric circuits, computerinstructions, etc. The apparatus 1000 may be implemented on a dedicatedcomputer, on a computer chip connected to the chemical reactionapparatus 2000 or installed thereon, on a computerized controllerconnected to the chemical reaction apparatus 2000 or installed thereon,etc.

Optionally, the chemical reaction is a Polymerase Chain Reaction (PCR),say a Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR), asdescribed in further detail hereinabove.

Apparatus 1000 includes a property value receiver 110, in communicationwith the data accumulator 270.

The property value receiver 110 receives values of a physical propertyof the chemical reaction, from the data accumulator 270, as described infurther detail hereinabove.

The apparatus 1000 further includes a linear function calculator 120.

The linear function calculator 120 is in communication with the propertyvalue receiver 110.

The linear function calculator 120 calculates a linear functionconnecting two of the received values. The two values pertain to a startand end of a time period, as described in further detail hereinbelow.

The time period may be a time period the chemical reaction is supposedto last for, a time period when a part of the chemical reaction takesplace, a time period long enough for the reaction to happen, a timeperiod spanning several cycles of the chemical reaction, etc.

Optionally, the linear function calculator 120 further allows a user ofthe apparatus 1000, to define the start and end of the time period, sayby inputting data defining the time period, as described in furtherdetail hereinabove.

The apparatus 1000 further includes a difference calculator 130, incommunication with the linear function calculator 120.

The difference calculator 130 calculates a difference between the linearfunction and two (or more) of the received values that pertain to thetime period. For example, the difference calculator 130 may calculate adifferences between the linear function and a curve based on the receivevalues, over a time period of the chemical reaction (or a segmentthereof), as described in further detail hereinbelow.

Apparatus 1000 further includes a transition point identifier 140, incommunication with the difference calculator 130.

The transition point identifier 140 identifies one or more transitionpoints of the chemical reaction, using the calculated difference, asdescribed in further detail hereinbelow. For example, the transitionpoint identifier 140 may identify the transition points, by finding thepoints where the difference between the linear function and the receivedvalues is maximal, minimal, etc.

Optionally, at least one of the transition points identified by thetransition point identifier 140 is a point in time of the chemicalreaction, when the value of the physical property starts increasingsubstantially exponentially.

Optionally, at least one of the transition points identified by thetransition point identifier 140 is a point in time of the chemicalreaction, when the value of the physical property stops increasingsubstantially exponentially.

Optionally, at least one of the transition points identified by thetransition point identifier 140 is a point in time of the chemicalreaction, when the value of the physical property starts decreasingsubstantially exponentially.

Optionally, at least one of the transition points identified by thetransition point identifier 140 is a point in time of the chemicalreaction, when the value of the physical property stops decreasingsubstantially exponentially.

Optionally, the apparatus 1000 further includes a control operationinitiator 250, in communication with the transition point identifier140.

When the transition point is identified, the control operation initiator250 initiates a control operation. The control operation may include,but is not limited to: initiating cooling of a chamber 210 where thechemical reaction takes place, opening of a pressure valve of thereaction chamber 210, instructing a PCR Robot to stop rotating, etc., asknown in the art.

Optionally, the apparatus 1000 further includes a monitoring datagenerator 290, in communication with the transition point identifier140. The monitoring data generator 290 generates monitoring data basedon the identified transition point.

Optionally, the monitoring data generator 290 further presents thegenerated data to a user, say using a computer screen, an SMS (ShortMessages Service) message on a cellular phone used by the user, amessage on a portable computer device such as a personal digitalassistant (PDA), or a notebook computer, etc.

Optionally, the monitoring data generator 290 further provides decisionsupport services to the user (say by presenting the generated data tothe user in a spreadsheet format such as a Microsoft® Excelspreadsheet).

Reference is now made to FIG. 3, which is a flowchart schematicallyillustrating a method for identifying transition points in a chemicalreaction, according to an exemplary embodiment of the present invention.

According to an exemplary embodiment, an exemplary method foridentifying transition points in a chemical reaction may be implementedusing electric circuits, computer instructions, etc. The method may beimplemented on a dedicated computer, on a computer chip connectable to alaboratory device (say to a PCR apparatus, as known in the art) orinstallable thereon, on a computerized controller (say a computerizedcontroller used in a chemical factory), etc., as described in furtherdetail hereinabove.

Optionally, the chemical reaction is a Polymerase Chain Reaction (PCR),say a Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR).

In the exemplary method, there are received 310 values of a physicalproperty of the chemical reaction, say by the physical property receiver110, as described in further detail hereinabove.

Optionally, the physical property values are received from thermometricsensors installed inside a chamber where the chemical reaction takesplace, from photometric sensors deployed in proximity to the chamber, orfrom other measurement devices, as described in further detailhereinabove.

For example, the chemical reaction may be a Quantitative FluorescentPolymerase Chain Reaction (QF-PCR). The Quantitative FluorescentPolymerase Chain Reaction is subjected to photometric measurements oflight emitted from the QF-PCR reaction chamber, during the chemicalreaction inside the QF-PCR chamber. The photometric measurement's valuesare then received 310, say by the property value receiver 110, asdescribed in further detail hereinabove.

Next, there is calculated 320 a linear function connecting two of thereceived values. The two values pertain to a start and end of a timeperiod, as described in further detail hereinbelow.

The time period may be a time period the chemical reaction is supposedto last for, a time period when a part of the chemical reaction takesplace, a time period long enough for the reaction to happen, a timeperiod spanning several cycles of the chemical reaction, etc.

Optionally, a user of the apparatus 1000 is allowed to define the startand end of the time period, say by inputting data defining the timeperiod in absolute (say from 10:00 PM to 10:15 PM) or relative (say 15minutes from start) terms.

Next, there is calculated 330 a difference between the linear functionand two (or more) of the received values that pertain to the timeperiod. For example, the difference calculator 130 may calculate 330 adifferences between the linear function and a curve based on the receivevalues, over a time period of the chemical reaction (or a segmentthereof), as described in further detail hereinbelow.

Finally, there is identified 340 one or more transition points of thechemical reaction, using the calculated difference, as described infurther detail hereinbelow. For example, the transition point identifier140 may identify 340 the transition points, by finding the points wherethe difference between the linear function and the received values ismaximal, minimal, etc.

Optionally, at least one of the identified 340 transition points is apoint in time of the chemical reaction, when the value of the physicalproperty starts increasing substantially exponentially.

Optionally, at least one of the identified 340 transition points is apoint in time of the chemical reaction, when the value of the physicalproperty stops increasing substantially exponentially.

Optionally, at least one of the identified 340 transition points is apoint in time of the chemical reaction, when the value of the physicalproperty starts decreasing substantially exponentially.

Optionally, at least one of the identified 340 transition points is apoint in time of the chemical reaction, when the value of the physicalproperty stops decreasing substantially exponentially.

Optionally, when the transition point is identified 340, there isindicated a beginning of a phase of the chemical reaction, an end of aphase of the chemical reaction, an end of a preliminary stabilizationphase of the chemical reaction, or any combination thereof.

Optionally, when the transition point is identified 340, there isinitiated a control operation. The control operation may include, but isnot limited to: initiating cooling of a chamber where the chemicalreaction takes place, opening of a pressure valve of a reaction chamber,instructing a PCR Robot to stop rotating, etc., as known in the art.

Optionally, there is further generated monitoring data based on theidentified transition point.

Optionally, the monitoring data is presented to a user. For example, themonitoring data may be presented on a computer screen, in an SMS (ShortMessages Service) message on a cellular phone used by the user, in amessage on a portable computer device such as a personal digitalassistant (PDA), or a notebook computer, etc.

Reference is now made to FIGS. 4A, 4B, 4C, 4D and 4E, which areexemplary graphs, illustrating an exemplary scenario of identifyingtransition points in a chemical reaction, according to an exemplaryembodiment of the present invention.

FIG. 4A graphically shows an exemplary curve 410, which representsvalues measured during a time period of a chemical reaction (say valuesreceived using the property value receiver 110), as described in furtherdetail hereinabove.

The x-axis corresponds to a time during the chemical reaction, whereasthe y-axis represents the value of the property of the chemicalreaction. That is to say that each point on curve 410 represents theproperty's value at a single point in time of the chemical reaction.

Reference is now made to FIG. 4B, which shows a curve of a first linearfunction 420, which connects a start point 450 and an end point 460 oncurve 410. The first linear function 420 may be calculated by the linearfunction calculator 120, as described in further detail hereinabove.

Reference is now made to FIG. 4C, which graphically shows a firstdifference curve 430. The first difference curve 430 represents thedifference between the first linear function 420 and curve 410. That isto say that the difference curve 430 represents the difference betweenthe first linear function 420 and the values of the physical property(say light emitted from a chemical chamber where the chemical reactiontakes place) during the time period between the two points 450, 460.

Optionally, the difference represented by the first difference curve 430is calculated by the difference calculator 130, as described in furtherdetail hereinabove.

One or more extremum points of the difference curve 430, say a minimumpoint 431 and a maximum point 432, indicate the points in time of thechemical reaction (i.e. x-values) when transition points of the chemicalreaction occur.

Consequently, points 411, 412 on curve 410, which correspond to theminimum point 431 and the maximum point 432, respectively, areidentified as two transition points of the chemical reaction.

Optionally, in each of the transition points 411, 412, the value of thephysical property starts decreasing substantially exponentially, stopsdecreasing substantially exponentially, starts increasing substantiallyexponentially, or stops increasing substantially exponentially, etc., asdescribed in further detail hereinabove. That is to say that typically,in the transition point, the chemical reaction shifts from asubstantially exponential phase into a substantially linear phase, orvise versa.

A method according to exemplary embodiment of the present invention maybe applied on the whole chemical reaction (say on the whole of curve410), and than on specific parts of the chemical reaction (say oncertain intervals of the curve 410).

Reference is now made to FIG. 4D, which graphically shows a secondlinear function 440, which connects the first transition point 411(which starts the exponential phase, which ends at the second transitionpoint 412), and point 450.

The upper part of FIG. 4D shows curve 410 as it appears in FIG. 4A,whereas the lower part of FIG. 4D shows the curve 410 and the secondlinear function 440 in a co-ordinate system where the y-coordinate isre-scaled, so as to illustrate more clearly the initial part of thecurve 410.

Reference is now made to FIG. 4E having a upper part which graphicallyshows a second difference curve 470 which represents the differencebetween the second linear curve and the received values (i.e. curve410).

Optionally, the difference represented by the second difference curve470 is calculated by the difference calculator 130, as described infurther detail hereinabove.

The second difference function 470 has a maximum 475 and a minimum 476.

The maximum 475 and minimum 476 are used to identify the chemicalreaction's transition points 415, 416, on curve 410, as shown in thelower part of FIG. 4E.

In one example, transition points 415 corresponds to a start of apreliminary phase where ingredients are added to the reaction, and causethe physical property's values (say light emitted from the chemicalreaction's chamber) to fluctuate. Transition point 416 may correspond toa phase where the added ingredients reach an even distribution in thereaction chamber, which causes the physical property to stabilize.

Reference is now made to FIG. 5, which is a block diagram schematicallyillustrating a computer readable medium storing computer executableinstructions for performing steps of identifying transition points in achemical reaction, according to an exemplary embodiment of the presentinvention.

According to an exemplary embodiment of the present invention, there isprovided a computer readable medium 5000 such as a CD-ROM, a USB-Memory,a Portable Hard Disk, a diskette, etc. The computer readable mediumstores computer executable instructions, for performing steps ofidentifying transition points in a chemical reaction, according to anexemplary embodiment of the present invention.

Upon execution by a computer, the instructions receive 510 values of aphysical property of the chemical reaction.

Optionally, the physical property values are received from thermometricsensors installed inside a chamber where the chemical reaction takesplace, from photometric sensors deployed in proximity to the chamber, orfrom other measurement devices, as described in further detailhereinabove.

For example, the chemical reaction may be a Quantitative FluorescentPolymerase Chain Reaction (QF-PCR). The Quantitative FluorescentPolymerase Chain Reaction is subjected to photometric measurements oflight emitted from the QF-PCR reaction chamber, during the chemicalreaction inside the QF-PCR chamber. The photometric measurement's valuesare then received 510, as described in further detail hereinabove.

Then, the instructions calculate 520 a linear function connecting two ofthe received values. The two values pertain to a start and end of a timeperiod, as described in further detail hereinbelow.

The time period may be a time period the chemical reaction is supposedto last for, a time period when a part of the chemical reaction takesplace, a time period long enough for the reaction to happen, a timeperiod spanning several cycles of the chemical reaction, etc.

Optionally, using some of the instructions, a user is allowed to definethe start and end of the time period, say by inputting data defining thetime period, as described in further detail hereinabove.

Next, the instructions calculate 530 a difference between the linearfunction and two (or more) of the received values that pertain to thetime period. For example, the instructions may calculate a differencesbetween the linear function and a curve based on the receive values,over a time period of the chemical reaction (or a segment thereof), asdescribed in further detail hereinbelow.

Finally, the instructions identify 540 one or more transition points ofthe chemical reaction, using the calculated difference, as described infurther detail hereinbelow. For example, the instructions may identify540 the transition points, by finding the points where the differencebetween the linear function and the received values is maximal, minimal,etc.

Optionally, when the transition point is identified 540, theinstructions further indicate that a phase of the chemical reactionbegins, that a phase of the chemical reaction ends, that a preliminarystabilization phase of the chemical reaction ends, etc.

Optionally, when the transition point is identified 540, theinstructions further initiate a control operation. The control operationmay include, but is not limited to: initiating cooling of a chemicalreaction chamber, opening of a pressure valve of a chemical reactionchamber, instructing a PCR Robot to stop rotating, etc.

Optionally, the instructions further generate monitoring data based onthe identified transition point.

Optionally, the instructions further present the monitoring data to auser. For example, the monitoring data may be presented on a computerscreen, in an SMS (Short Messages Service) message on a cellular phoneused by the user, in a message on a portable computer device such as apersonal digital assistant (PDA), or a notebook computer, etc.

It is expected that during the life of this patent many relevant devicesand systems will be developed and the scope of the terms herein,particularly of the terms “Polymerase Chain Reaction”, “QuantitativeFluorescent Polymerase Chain Reaction” and “Fluorescence”, is intendedto include all such new technologies a priori.

It is appreciated that certain features of the invention, which are, forclarity, described in the context of separate embodiments, may also beprovided in combination in a single embodiment. Conversely, variousfeatures of the invention, which are, for brevity, described in thecontext of a single embodiment, may also be provided separately or inany suitable subcombination.

Although the invention has been described in conjunction with specificembodiments thereof, it is evident that many alternatives, modificationsand variations will be apparent to those skilled in the art.Accordingly, it is intended to embrace all such alternatives,modifications and variations that fall within the spirit and broad scopeof the appended claims.

All publications, patents and patent applications mentioned in thisspecification are herein incorporated in their entirety by referenceinto the specification, to the same extent as if each individualpublication, patent or patent application was specifically andindividually indicated to be incorporated herein by reference. Inaddition, citation or identification of any reference in thisapplication shall not be construed as an admission that such referenceis available as prior art to the present invention.

1. A chemical reaction system, the system comprising: a reactionapparatus, comprising at least one sensor configured to measure aplurality of values of a physical property of a chemical reaction anelectronic computing device, in communication with said reactionapparatus, configured to process data; a property value receiver,implemented at least in part on said electronic computing device,configured to receive the plurality of values of the physical propertyof the chemical reaction; a linear function calculator, associated withsaid property value receiver, configured to calculate a linear functionspanning over at least a part of the chemical reaction, the at least apart of the chemical reaction spanning over a predefined time periodhaving a start and end, the linear function connecting two of thereceived values, the two values pertaining to the start and end of thetime period, the linear function having a first value pertaining to thestart of the time period and being a same value as the received valuepertaining to the start of the time period, and a second valuepertaining to the end of the time period and being a same value as thereceived value pertaining to the end of the time period; a differencecalculator, associated with said linear function calculator, configuredto calculate a difference between the linear function and a plurality ofthe received values pertaining to the part; a transition pointidentifier, associated with said difference calculator, configured toidentify at least one transition point of the chemical reaction withinthe part, using the calculated difference; and a control operationinitiator, associated with said transition point identifier, configuredto initiate a control operation upon the transition point beingidentified.
 2. An apparatus for identifying transition points in achemical reaction, the apparatus comprising: an electronic computingdevice configured to process data; a property value receiver,implemented at least in part on said electronic computing device,configured to receive a plurality of values of a physical property ofthe chemical reaction from a reaction apparatus; a linear functioncalculator, associated with said property value receiver, configured tocalculate a linear function spanning over at least a part of thechemical reaction, the at least a part of the chemical reaction spanningover a predefined time period having a start and end, the linearfunction connecting two of the received values, the two valuespertaining to the start and end of the time period, the linear functionhaving a first value pertaining to the start of the time period andbeing a same value as the received value pertaining to the start of thetime period, and a second value pertaining to the end of the time periodand being a same value as the received value pertaining to the end ofthe time period; a difference calculator, associated with said linearfunction calculator, configured to calculate a difference between thelinear function and a plurality of the received values pertaining to thepart; a transition point identifier, associated with said differencecalculator, configured to identify at least one transition point of thechemical reaction within the part, using the calculated difference; anda control operation initiator, associated with said transition pointidentifier, configured to initiate a control operation upon thetransition point being identified.
 3. The apparatus of claim 2, whereinthe values are photometric measurement values.
 4. The apparatus of claim2, wherein the values of the physical property start increasingsubstantially exponentially at the identified transition point.
 5. Theapparatus of claim 2, wherein the values of the physical property stopincreasing substantially exponentially at the identified transitionpoint.
 6. The apparatus of claim 2, wherein the values of the physicalproperty start decreasing substantially exponentially at the identifiedtransition point.
 7. The apparatus of claim 2, wherein the values of thephysical property stop decreasing substantially exponentially at theidentified transition point.
 8. The apparatus of claim 2, furthercomprising a phase indicator, associated with said transition pointidentifier, configured to indicate a beginning of a phase of thechemical reaction upon the transition point being identified.
 9. Theapparatus of claim 2, further comprising a phase indicator, associatedwith said transition point identifier, configured to indicate an end ofa phase of the chemical reaction upon the transition point beingidentified.
 10. The apparatus of claim 2, further comprising a phaseindicator, associated with said transition point identifier, configuredto indicate an end of a preliminary stabilization phase of the chemicalreaction upon the transition point being identified.
 11. The apparatusof claim 2, further comprising a monitoring data generator, associatedwith said transition point identifier, configured to generate monitoringdata based on the identified transition point and to present themonitoring data to a user of the reaction apparatus.
 12. The apparatusof claim 2, further comprising a measurement device, associated withsaid property value receiver, configured to measure the values of thephysical property.
 13. A computer implemented method for identifyingtransition points in a chemical reaction, the method comprising stepsthe computer is programmed to perform, the steps comprising: a)receiving a plurality of values of a physical property of the chemicalreaction from a reaction apparatus; b) calculating a linear functionspanning over at least a part of the chemical reaction, the at least apart of the chemical reaction spanning over a predefined time periodhaving a start and end, the linear function connecting two of thereceived values, the two values pertaining to the start and end of thetime period, the linear function having a first value pertaining to thestart of the time period and being a same value as the received valuepertaining to the start of the time period, and a second valuepertaining to the end of the time period and being a same value as thereceived value pertaining to the end of the time period; c) calculatinga difference between the linear function and a plurality of the receivedvalues pertaining to the part; d) identifying at least one transitionpoint of the chemical reaction within the part, using the calculateddifference; and e) initiating a control operation upon said identifyingof the transition point.
 14. The method of claim 13, further comprisingindicating a beginning of a phase of the chemical reaction upon saididentifying of the transition point.
 15. The method of claim 13, furthercomprising indicating an end of a phase of the chemical reaction uponsaid identifying of the transition point.
 16. The method of claim 13,further comprising indicating an end of a preliminary stabilizationphase of the chemical reaction upon said identifying of the transitionpoint.
 17. The method of claim 13, further comprising generatingmonitoring data that is based on the identified transition point andpresenting the monitoring data to a user of the reaction apparatus. 18.The method of claim 13, further comprising measuring the values of thephysical property.
 19. A computer readable medium storing computerexecutable instructions for performing steps of identifying transitionpoints in a chemical reaction, the steps comprising: a) receiving aplurality of values of a physical property of the chemical reaction froma reaction apparatus; b) calculating a linear function spanning over atleast a part of the chemical reaction, the at least a part of thechemical reaction spanning over a predefined time period having a startand end, the linear function connecting two of the received values, thetwo values pertaining to the start and end of the time period, thelinear function having a first value pertaining to the start of the timeperiod and being a same value as the received value pertaining to thestart of the time period, and a second value pertaining to the end ofthe time period and being a same value as the received value pertainingto the end of the time period; c) calculating a difference between thelinear function and a plurality of the received values pertaining to thepart; d) identifying at least one transition point of the chemicalreaction within the part, using the calculated difference; and e)initiating a control operation upon said identifying of the transitionpoint.
 20. The method of claim 19, further comprising instructing arobot based on the identified transition point.